As stated by Dr. John C. Wingfield, the ultimate frontier in biology is taking the lab to the field to study organisms in their environments. Dr. Wingfield's assessment is even more important in the study of aquatic environments. Aqueous microbes constitute a hidden majority of life on earth, and comprise the most diverse group of organisms on our planet. They are the key players in global carbon cycling and other biogeochemical processes that broadly affect the health of the planet. However, they are among the most under-studied life forms because of the vastness of their often inaccessible habitats and their ‘patchy’ distribution.
Aquatic microbes are interesting on a species level as well as on a community level. On a species level, certain harmful algae are of public interest due to their ability to infect fish populations and transmit toxins to humans and the ecosystems. Others, such as Naegleria fowleri, a freshwater amoeba, infect humans directly often leading to death. Aquatic microbes are also very interesting on a community scale. Indeed, key questions of environmental microbiology include “who are the members of the microbial community” and “which members are the major contributors to community dynamics.” Understanding these key microbial players and the dynamic interactions among them and their environments are of great societal interest. Models regarding ocean acidification, carbon cycling, climate change, species adaptation, and the effects of geochemical perturbations are underdeveloped and require increased understanding of microbial population dynamics. The technical requirements for monitoring microbes in their natural environment are extremely demanding, at least because they are to be deployed remotely and conduct automatic in situ measurements.
While development of technologies for systems biology has made it more feasible to study the interaction of microorganism in aquatic environment, much of the technological developments are limited to in-lab instruments. Although there are bench-top microfluidic platforms for analysis of aquatic organisms, these platforms are unsuitable for autonomous microbial genomic profiling. Unlike bench-top instruments, instruments for autonomous in situ genomic instruments require robust fluidic handling, low energy consumption, long-term reagent storage (especially for enzymes), and easy portability. Additionally, being situated in the field, autonomous in situ genomic instruments cannot reply on pressurized gas, continuous vacuum, refrigeration, or manual intervention.
In addition to obstacles in the workability of an automatic in situ genomic instrument, there are heavy burdens in maintaining the function of such an instrument. In situ genomic sensors are expensive and require large payloads of batteries to achieve relatively short deployment time. Unfortunately, the assay performance is often insufficient. Accordingly, there is a need to develop an in situ device with improved energy consumption, reduced running costs, increased per-unit throughput that at least retains the analytical assay performance of existing in situ genomic sensors.